Katina I. Spanier

CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species

CREsted is a software package for modeling and designing cell type-specific enhancers using deep learning, validated across tissues and species.

HyDrop v2: Scalable atlas construction for training sequence-to-function models

The paper introduces HyDrop v2, a microfluidic system for generating large scATAC-seq atlases, and shows its data is comparable to commercial platforms for training sequence-to-function models.

Spatial transcriptomics in the adult Drosophila brain and body

The paper applies spatial transcriptomics to the adult Drosophila brain and body to map mRNA locations and integrate with single-cell data.

Cell type directed design of synthetic enhancers

This study uses deep learning to design synthetic enhancers that target specific cell types in fruit flies and humans, revealing the enhancer code as optimal TF activator motifs and absence of repressor motifs.

Cell type diversity in a developing octopus brain

The paper profiles cell diversity in the paralarval octopus brain to create a cell type atlas and identifies molecular similarities between octopus and fly glial cells.

Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

The paper creates a single-cell transcriptomic atlas of the adult fruit fly, identifying over 250 cell types and analyzing gene signatures and sexual dimorphism across tissues.

Decoding gene regulation in the fly brain

The paper identifies regulatory regions and gene regulatory networks in Drosophila brain cell types using chromatin accessibility and transcriptome data.

Single-cell gene regulatory network analysis reveals new melanoma cell states and transition trajectories during phenotype switching

The paper identifies an intermediate cell state in melanoma through single-cell RNA-seq and ATAC-seq, revealing a gene regulatory network that governs phenotype switching and potential therapeutic targets.

A single-cell catalogue of regulatory states in the ageing Drosophila brain

This study creates a single-cell transcriptome catalogue of the Drosophila brain across its lifespan, revealing regulatory erosion and identifying novel neuronal states linked to ageing.